Related papers: Horizontal gene transfer: numerical comparison bet…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
We revisit the SICA (Susceptible-Infectious-Chronic-AIDS) mathematical model for transmission dynamics of the human immunodeficiency virus (HIV) with varying population size in a homogeneously mixing population. We consider SICA models…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
Hybrid dynamical systems with nonlinear dynamics are one of the most general modeling tools for representing robotic systems, especially contact-rich systems. However, providing guarantees regarding the safety or performance of nonlinear…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
Plasmids are major players in Horizontal Gene Transfer mechanisms, hence they are highly variable in their gene content and length. We propose a model for the fitness of a plasmid as a function of its length, which predicts diminishing…
The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been…
Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time…
Simplicial complex (SC) representation is an elegant mathematical framework for representing the effect of complexes or groups with higher-order interactions in a variety of complex systems ranging from brain networks to social…
Studies about epidemic modelling have been conducted since before 19th century. Both deterministic and stochastiic model were used to capture the dynamic of infection in the population. The purpose of this project is to investigate the…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
In the paper, an evolutionary approach to test generation for functional BIST is considered. The aim of the proposed scheme is to minimize the test data volume by allowing the device's microprogram to test its logic, providing an…
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there has been very little study of the extent…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician's toolbox as an alternative sampling method in settings when standard Metropolis-Hastings is inefficient. HMC generates a Markov chain on an augmented…
Habitat loss is one of the biggest threats facing plant species nowadays. We formulate a simple mathematical model of seed dispersal on reduced habitats to discuss survival of the species in relation to the habitat size and seeds production…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
In real-world applications, it is often expensive and time-consuming to obtain labeled examples. In such cases, knowledge transfer from related domains, where labels are abundant, could greatly reduce the need for extensive labeling…
Several low-dimensional systems show a crossover from diffusive to ballistic heat transport when system size is decreased. Although there is some phenomenological understanding of this crossover phenomena in the coarse grained level, a…